From 3401d5ca738dd337cf16b7204575d9dd3c7d5589 Mon Sep 17 00:00:00 2001
From: Duncan Leggat <ccaedle@ucl.ac.uk>
Date: Mon, 12 Feb 2024 18:28:33 +0000
Subject: [PATCH 1/3] Adding in VVUQ campaign functions

---
 FabNESO/__init__.py                           |  18 +-
 FabNESO/run_vvuq_instance.sh                  |   9 +
 FabNESO/tasks.py                              | 191 +++++++++++++++++-
 config_files/vvuq_example/conditions.template |  77 +++++++
 config_files/vvuq_example/mesh.xml            | 155 ++++++++++++++
 config_files/vvuq_example/vvuq_parameters.txt |  17 ++
 requirements.txt                              |   2 +
 7 files changed, 466 insertions(+), 3 deletions(-)
 create mode 100755 FabNESO/run_vvuq_instance.sh
 create mode 100644 config_files/vvuq_example/conditions.template
 create mode 100644 config_files/vvuq_example/mesh.xml
 create mode 100644 config_files/vvuq_example/vvuq_parameters.txt

diff --git a/FabNESO/__init__.py b/FabNESO/__init__.py
index c5bfed2..9e82704 100644
--- a/FabNESO/__init__.py
+++ b/FabNESO/__init__.py
@@ -1,9 +1,23 @@
 """Neptune Exploratory SOftware (NESO) plugin for FabSim3."""
 
 try:
-    from .tasks import neso, neso_ensemble, neso_vbmc, neso_write_field
+    from .tasks import (
+        neso,
+        neso_ensemble,
+        neso_vbmc,
+        neso_vvuq_campaign,
+        neso_write_field,
+        single_run_vvuq,
+    )
 
-    __all__ = ["neso", "neso_ensemble", "neso_vbmc", "neso_write_field"]
+    __all__ = [
+        "neso",
+        "neso_ensemble",
+        "neso_vbmc",
+        "neso_write_field",
+        "neso_vvuq_campaign",
+        "single_run_vvuq",
+    ]
 
 except ImportError:
     import warnings
diff --git a/FabNESO/run_vvuq_instance.sh b/FabNESO/run_vvuq_instance.sh
new file mode 100755
index 0000000..74e6414
--- /dev/null
+++ b/FabNESO/run_vvuq_instance.sh
@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+
+echo fabsim $1 single_run_vvuq:$PWD,solver=$4,processes=$5,nodes=$6,cpus_per_process=$7,wall_time=$8,neso_outfile=$9
+
+pwd
+
+cp $3 .
+
+fabsim $1 single_run_vvuq:$PWD,solver=$4,processes=$5,nodes=$6,cpus_per_process=$7,wall_time=$8,neso_outfile=$9
diff --git a/FabNESO/tasks.py b/FabNESO/tasks.py
index 9c93e4f..f0d90c1 100644
--- a/FabNESO/tasks.py
+++ b/FabNESO/tasks.py
@@ -7,13 +7,23 @@
 import re
 import shutil
 import time
+from ast import literal_eval
 from contextlib import nullcontext
 from pathlib import Path
 from tempfile import TemporaryDirectory
 from typing import Any
 
+import chaospy as cp
+import easyvvuq as uq
 import numpy as np
 import pyvbmc
+from easyvvuq.actions import (
+    Actions,
+    CreateRunDirectory,
+    Decode,
+    Encode,
+    ExecuteLocal,
+)
 
 try:
     from fabsim.base import fab
@@ -301,7 +311,7 @@ def neso_vbmc(
     **vbmc_parameters: str,
 ) -> None:
     """
-    Run variational Bayesian Monte Carlo (VBMC) to calibrate NESO solver parameters.
+    Run variational Bayesian Monte Carlo (VBMC) to calibrate NESO solver parametes.
 
     The VBMC algorithm (Acerbi, 2018) is an approximate Bayesian inference method for
     efficient parameter calibration in expensive to simulate models. Here we use the
@@ -571,3 +581,182 @@ def log_density(
         (config_dict["initial_run"] - observed_results["field_value"]) ** 2
         / (2 * config_dict["observation_noise_std"] ** 2)
     ).sum()
+
+
+def _parse_vvuq_parameters(
+    vvuq_param_file: Path,
+) -> tuple[dict[Any, dict[str, float]], dict[str, Any], list[str]]:
+    # read the inpurt file
+    with Path.open(vvuq_param_file) as f:
+        data = f.read()
+    d = literal_eval(data)
+    vvuq_params = {}
+    parameter_variations = {}
+    for parameter, param_values in d["parameters"].items():
+        vvuq_params[parameter] = {
+            "type": "float",
+            "default": param_values[0],
+        }
+        vary_length = 3
+        if len(param_values) == vary_length:
+            # Make the chaospy distribution. Possibly to be able to edit this later?
+            parameter_variations[parameter] = cp.Uniform(
+                param_values[1], param_values[2]
+            )
+    output_columns = d["output_columns"]
+    return (vvuq_params, parameter_variations, output_columns)
+
+
+@fab.task
+@fab.load_plugin_env_vars("FabNESO")
+def single_run_vvuq(
+    config: str,
+    solver: str = "Electrostatic2D3V",
+    processes: str | int = 4,
+    nodes: str | int = 1,
+    cpus_per_process: str | int = 1,
+    wall_time: str = "00:15:00",
+    neso_outfile: str = "Electrostatic2D3V_line_field_evaluations.h5part",
+) -> None:
+    """
+    Run a single instance of the VVUQ campaign.
+
+    Run an instance of the VVUQ campaign using configurations in the designated solver.
+    The conditions and mesh are, by design, the defaults. When the iteration is done,
+    copy the NESO output to the local directory for later decoding through VVUQ.
+
+
+    Args:
+        config: Directory with single run configuration information.
+
+    Keyword Args:
+        solver: Which NESO solver to use.
+        processes: Number of processes to run.
+        nodes: Number of nodes to run on. Only applicable when running on a multi-node
+            system.
+        cpus_per_process: Number of processing units to use per process. Only
+            applicable when running on a multi-node system.
+        wall_time: Maximum time to allow job to run for. Only applicable when submitting
+            to a job scheduler.
+        neso_outfile: Name of the output file the NESO solver produces, to copy across
+            to the local directory.
+
+    """
+    # If we're running remotely, tell the submission to wait until done
+    if "archer2" in fab.env.remote:
+        fab.update_environment(
+            {
+                "job_dispatch": "cd /work/$project/$project/$username ; sbatch --wait",
+            }
+        )
+
+    # Run an instance of NESO
+    neso(
+        config,
+        solver=solver,
+        processes=processes,
+        nodes=nodes,
+        cpus_per_process=cpus_per_process,
+        wall_time=wall_time,
+    )
+    # Retrieve the results
+    fab.fetch_results()
+
+    # Move the results to the local VVUQ directory for further processing
+    local_results_dir = Path(fab.env.job_results_local) / template(
+        fab.env.job_name_template
+    )
+    shutil.copyfile(local_results_dir / neso_outfile, neso_outfile)
+
+
+@fab.task
+@fab.load_plugin_env_vars("FabNESO")
+def neso_vvuq_campaign(  # noqa: PLR0913
+    vvuq_config: str,
+    conditions_template: str = "conditions.template",
+    vvuq_parameters: str = "vvuq_parameters.txt",
+    vvuq_script: str = "run_vvuq_instance.sh",
+    neso_mesh_file: str = "mesh.xml",
+    output_dir: str = "neso_pce/",
+    neso_outfile: str = "Electrostatic2D3V_line_field_evaluations.h5part",
+    solver: str = "Electrostatic2D3V",
+    processes: str | int = 4,
+    nodes: str | int = 1,
+    cpus_per_process: str | int = 1,
+    wall_time: str = "00:15:00",
+) -> None:
+    """
+    Run a VVUQ campaign on a NESO solver.
+
+    Args:
+        vvuq_config: Directory with VVUQ parameters, conditions template file, and mesh
+            configuration.
+
+    Keyword Args:
+        conditions_template: A template NESO conditions file. Parameters that are to be
+            varied are indicated with a $ sign.
+        vvuq_parameters: A file in the vvuq_config directory containing a dict with
+            "parameters" that correspond to the parameters to replace in template file,
+            "output_columns" that are the NESO outputs that VVUQ should read for its
+            analysis
+        neso_mesh_file: Name of mesh XML in vvuq_config directory.
+        output_dir: Directory in which to carry out the VVUQ campaign.
+        neso_outfile: Name of the output file the NESO solver produces, to copy across
+            to the local directory.
+        solver: Which NESO solver to use.
+        processes: Number of processes to run.
+        nodes: Number of nodes to run on. Only applicable when running on a multi-node
+            system.
+        cpus_per_process: Number of processing units to use per process. Only
+            applicable when running on a multi-node system.
+        wall_time: Maximum time to allow job to run for. Only applicable when submitting
+            to a job scheduler.
+
+    """
+    path_to_vvuq_configs = Path(fab.find_config_file_path(vvuq_config))
+
+    # Extract the parameters for the conditions template and variations from the config
+    params, vary, outputs_to_read = _parse_vvuq_parameters(
+        path_to_vvuq_configs / vvuq_parameters
+    )
+
+    # Make an encoder
+    encoder = uq.encoders.GenericEncoder(
+        path_to_vvuq_configs / conditions_template,
+        delimiter="$",
+        target_filename="conditions.xml",
+    )
+
+    # Make the VVUQ decoder - this should be more generic!
+    decoder = uq.decoders.HDF5(
+        target_filename=neso_outfile,
+        output_columns=outputs_to_read,
+    )
+
+    # Get the path for this plugin,
+    vvuq_run_path = Path(fab.get_plugin_path("FabNESO")) / "FabNESO" / vvuq_script
+
+    # The script that runs the individual NESO instances
+    execute_local = ExecuteLocal(
+        f"{vvuq_run_path} {fab.env.remote} {vvuq_config} "
+        f"{path_to_vvuq_configs / neso_mesh_file} {solver} {processes} "
+        f"{nodes} {cpus_per_process} {wall_time} {neso_outfile}"
+    )
+
+    # Put together the actions required for the VVUQ campaign
+    actions = Actions(
+        CreateRunDirectory("/tmp", flatten=True),  # noqa: S108
+        Encode(encoder),
+        execute_local,
+        Decode(decoder),
+    )
+
+    # Make the VVUQ campaign
+    campaign = uq.Campaign(name=output_dir, params=params, actions=actions)
+
+    # Make and attach a sampler to the campaign
+    my_sampler = uq.sampling.PCESampler(vary)
+    campaign.set_sampler(my_sampler)
+
+    # Run VVUQ
+    campaign.execute(sequential=True).collate()
diff --git a/config_files/vvuq_example/conditions.template b/config_files/vvuq_example/conditions.template
new file mode 100644
index 0000000..9f68042
--- /dev/null
+++ b/config_files/vvuq_example/conditions.template
@@ -0,0 +1,77 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<NEKTAR xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:noNamespaceSchemaLocation="http://www.nektar.info/schema/nektar.xsd">
+
+    <EXPANSIONS>
+        <E COMPOSITE="C[1]" NUMMODES="2" TYPE="MODIFIED" FIELDS="u" />
+        <E COMPOSITE="C[1]" NUMMODES="2" TYPE="MODIFIED" FIELDS="rho" />
+    </EXPANSIONS>
+
+    <CONDITIONS>
+
+        <SOLVERINFO>
+            <I PROPERTY="EQTYPE" VALUE="PoissonPIC" />
+            <I PROPERTY="Projection" VALUE="Continuous" />
+        </SOLVERINFO>
+
+        <GLOBALSYSSOLNINFO>
+            <V VAR="u">
+            <I PROPERTY="GlobalSysSoln" VALUE="IterativeStaticCond" />
+            <I PROPERTY="IterativeSolverTolerance" VALUE="1e-8"/>
+            </V>
+        </GLOBALSYSSOLNINFO>
+
+        <PARAMETERS>
+            <P> Lambda = 0.0 </P>
+            <P> epsilon = -1.0 </P>
+            <P> num_particles_total = $NUMBER_PARTICLES </P>
+            <P> num_particles_per_cell = -1 </P>
+            <P> particle_time_step = 0.001 </P>
+            <P> particle_num_time_steps = $TIME_STEPS </P>
+            <P> particle_num_write_particle_steps = 0 </P>
+            <P> particle_num_write_field_energy_steps = 20 </P>
+            <P> particle_num_write_field_steps = $WRITE_FIELD_STEPS </P>
+            <P> particle_num_print_steps = 40 </P>
+            <P> particle_distribution_position = 2 </P>
+            <P> particle_initial_velocity = $INIT_VELOCITY </P>
+            <P> particle_charge_density = $CHARGE_DENSITY </P>
+            <P> particle_number_density = $NUMBER_DENSITY </P>
+            <P> line_field_deriv_evaluations_step = $LINE_STEP </P>
+            <P> line_field_deriv_evaluations_numx = $LINE_NUMX </P>
+            <P> line_field_deriv_evaluations_numy = $LINE_NUMY </P>
+        </PARAMETERS>
+
+        <VARIABLES>
+            <V ID="0"> u </V>
+            <V ID="1"> rho </V>
+        </VARIABLES>
+
+        <BOUNDARYREGIONS>
+            <B ID="1"> C[100] </B>
+            <B ID="2"> C[200]  </B>
+            <B ID="3"> C[300] </B>
+            <B ID="4"> C[400] </B>
+        </BOUNDARYREGIONS>
+
+        <BOUNDARYCONDITIONS>
+            <REGION REF="1">
+                <P VAR="u" VALUE="[3]" />
+                <P VAR="rho" VALUE="[3]" />
+            </REGION>
+            <REGION REF="2">
+                <P VAR="u" VALUE="[4]" />
+                <P VAR="rho" VALUE="[4]" />
+            </REGION>
+            <REGION REF="3">
+                <P VAR="u" VALUE="[1]" />
+                <P VAR="rho" VALUE="[1]" />
+            </REGION>
+            <REGION REF="4">
+                <P VAR="u" VALUE="[2]" />
+                <P VAR="rho" VALUE="[2]" />
+            </REGION>
+        </BOUNDARYCONDITIONS>
+
+    </CONDITIONS>
+
+</NEKTAR>
diff --git a/config_files/vvuq_example/mesh.xml b/config_files/vvuq_example/mesh.xml
new file mode 100644
index 0000000..dba3c9f
--- /dev/null
+++ b/config_files/vvuq_example/mesh.xml
@@ -0,0 +1,155 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<NEKTAR>
+    <GEOMETRY DIM="2" SPACE="2">
+        <VERTEX>
+            <V ID="0">0.00000000e+00 0.00000000e+00 0.00000000e+00</V>
+            <V ID="1">5.00000000e-02 0.00000000e+00 0.00000000e+00</V>
+            <V ID="2">5.00000000e-02 1.00000000e-02 0.00000000e+00</V>
+            <V ID="3">0.00000000e+00 1.00000000e-02 0.00000000e+00</V>
+            <V ID="4">1.00000000e-01 0.00000000e+00 0.00000000e+00</V>
+            <V ID="5">1.00000000e-01 1.00000000e-02 0.00000000e+00</V>
+            <V ID="6">1.50000000e-01 0.00000000e+00 0.00000000e+00</V>
+            <V ID="7">1.50000000e-01 1.00000000e-02 0.00000000e+00</V>
+            <V ID="8">2.00000000e-01 0.00000000e+00 0.00000000e+00</V>
+            <V ID="9">2.00000000e-01 1.00000000e-02 0.00000000e+00</V>
+            <V ID="10">2.50000000e-01 0.00000000e+00 0.00000000e+00</V>
+            <V ID="11">2.50000000e-01 1.00000000e-02 0.00000000e+00</V>
+            <V ID="12">3.00000000e-01 0.00000000e+00 0.00000000e+00</V>
+            <V ID="13">3.00000000e-01 1.00000000e-02 0.00000000e+00</V>
+            <V ID="14">3.50000000e-01 0.00000000e+00 0.00000000e+00</V>
+            <V ID="15">3.50000000e-01 1.00000000e-02 0.00000000e+00</V>
+            <V ID="16">4.00000000e-01 0.00000000e+00 0.00000000e+00</V>
+            <V ID="17">4.00000000e-01 1.00000000e-02 0.00000000e+00</V>
+            <V ID="18">4.50000000e-01 0.00000000e+00 0.00000000e+00</V>
+            <V ID="19">4.50000000e-01 1.00000000e-02 0.00000000e+00</V>
+            <V ID="20">5.00000000e-01 0.00000000e+00 0.00000000e+00</V>
+            <V ID="21">5.00000000e-01 1.00000000e-02 0.00000000e+00</V>
+            <V ID="22">5.50000000e-01 0.00000000e+00 0.00000000e+00</V>
+            <V ID="23">5.50000000e-01 1.00000000e-02 0.00000000e+00</V>
+            <V ID="24">6.00000000e-01 0.00000000e+00 0.00000000e+00</V>
+            <V ID="25">6.00000000e-01 1.00000000e-02 0.00000000e+00</V>
+            <V ID="26">6.50000000e-01 0.00000000e+00 0.00000000e+00</V>
+            <V ID="27">6.50000000e-01 1.00000000e-02 0.00000000e+00</V>
+            <V ID="28">7.00000000e-01 0.00000000e+00 0.00000000e+00</V>
+            <V ID="29">7.00000000e-01 1.00000000e-02 0.00000000e+00</V>
+            <V ID="30">7.50000000e-01 0.00000000e+00 0.00000000e+00</V>
+            <V ID="31">7.50000000e-01 1.00000000e-02 0.00000000e+00</V>
+            <V ID="32">8.00000000e-01 0.00000000e+00 0.00000000e+00</V>
+            <V ID="33">8.00000000e-01 1.00000000e-02 0.00000000e+00</V>
+            <V ID="34">8.50000000e-01 0.00000000e+00 0.00000000e+00</V>
+            <V ID="35">8.50000000e-01 1.00000000e-02 0.00000000e+00</V>
+            <V ID="36">9.00000000e-01 0.00000000e+00 0.00000000e+00</V>
+            <V ID="37">9.00000000e-01 1.00000000e-02 0.00000000e+00</V>
+            <V ID="38">9.50000000e-01 0.00000000e+00 0.00000000e+00</V>
+            <V ID="39">9.50000000e-01 1.00000000e-02 0.00000000e+00</V>
+            <V ID="40">1.00000000e+00 0.00000000e+00 0.00000000e+00</V>
+            <V ID="41">1.00000000e+00 1.00000000e-02 0.00000000e+00</V>
+        </VERTEX>
+        <EDGE>
+            <E ID="0">0 1</E>
+            <E ID="1">1 2</E>
+            <E ID="2">2 3</E>
+            <E ID="3">3 0</E>
+            <E ID="4">1 4</E>
+            <E ID="5">4 5</E>
+            <E ID="6">5 2</E>
+            <E ID="7">4 6</E>
+            <E ID="8">6 7</E>
+            <E ID="9">7 5</E>
+            <E ID="10">6 8</E>
+            <E ID="11">8 9</E>
+            <E ID="12">9 7</E>
+            <E ID="13">8 10</E>
+            <E ID="14">10 11</E>
+            <E ID="15">11 9</E>
+            <E ID="16">10 12</E>
+            <E ID="17">12 13</E>
+            <E ID="18">13 11</E>
+            <E ID="19">12 14</E>
+            <E ID="20">14 15</E>
+            <E ID="21">15 13</E>
+            <E ID="22">14 16</E>
+            <E ID="23">16 17</E>
+            <E ID="24">17 15</E>
+            <E ID="25">16 18</E>
+            <E ID="26">18 19</E>
+            <E ID="27">19 17</E>
+            <E ID="28">18 20</E>
+            <E ID="29">20 21</E>
+            <E ID="30">21 19</E>
+            <E ID="31">20 22</E>
+            <E ID="32">22 23</E>
+            <E ID="33">23 21</E>
+            <E ID="34">22 24</E>
+            <E ID="35">24 25</E>
+            <E ID="36">25 23</E>
+            <E ID="37">24 26</E>
+            <E ID="38">26 27</E>
+            <E ID="39">27 25</E>
+            <E ID="40">26 28</E>
+            <E ID="41">28 29</E>
+            <E ID="42">29 27</E>
+            <E ID="43">28 30</E>
+            <E ID="44">30 31</E>
+            <E ID="45">31 29</E>
+            <E ID="46">30 32</E>
+            <E ID="47">32 33</E>
+            <E ID="48">33 31</E>
+            <E ID="49">32 34</E>
+            <E ID="50">34 35</E>
+            <E ID="51">35 33</E>
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+            <E ID="53">36 37</E>
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+            <E ID="56">38 39</E>
+            <E ID="57">39 37</E>
+            <E ID="58">38 40</E>
+            <E ID="59">40 41</E>
+            <E ID="60">41 39</E>
+        </EDGE>
+        <ELEMENT>
+            <Q ID="0">0 1 2 3</Q>
+            <Q ID="1">4 5 6 1</Q>
+            <Q ID="2">7 8 9 5</Q>
+            <Q ID="3">10 11 12 8</Q>
+            <Q ID="4">13 14 15 11</Q>
+            <Q ID="5">16 17 18 14</Q>
+            <Q ID="6">19 20 21 17</Q>
+            <Q ID="7">22 23 24 20</Q>
+            <Q ID="8">25 26 27 23</Q>
+            <Q ID="9">28 29 30 26</Q>
+            <Q ID="10">31 32 33 29</Q>
+            <Q ID="11">34 35 36 32</Q>
+            <Q ID="12">37 38 39 35</Q>
+            <Q ID="13">40 41 42 38</Q>
+            <Q ID="14">43 44 45 41</Q>
+            <Q ID="15">46 47 48 44</Q>
+            <Q ID="16">49 50 51 47</Q>
+            <Q ID="17">52 53 54 50</Q>
+            <Q ID="18">55 56 57 53</Q>
+            <Q ID="19">58 59 60 56</Q>
+        </ELEMENT>
+        <CURVED />
+        <COMPOSITE>
+            <C ID="1"> Q[0-19] </C>
+            <C ID="100"> E[0,4,7,10,13,16,19,22,25,28,31,34,37,40,43,46,49,52,55,58] </C>
+            <C ID="200"> E[59] </C>
+            <C ID="300"> E[2,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60] </C>
+            <C ID="400"> E[3] </C>
+        </COMPOSITE>
+        <DOMAIN>
+            <D ID="0"> C[1] </D>
+        </DOMAIN>
+    </GEOMETRY>
+    <Metadata>
+        <Provenance>
+            <GitBranch></GitBranch>
+            <GitSHA1>f1598d5e39f175acf388b90df392f76ff29d7f9d</GitSHA1>
+            <Hostname>L0211-XU</Hostname>
+            <NektarVersion>5.2.0</NektarVersion>
+            <Timestamp>23-Nov-2022 10:54:06</Timestamp>
+        </Provenance>
+        <NekMeshCommandLine>-v -m peralign:surf1=100:surf2=300:dir=y -m peralign:surf1=200:surf2=400:dir=x periodic_structured_cartesian_rectangle.msh periodic_structured_cartesian_rectangle.xml:xml:uncompress </NekMeshCommandLine>
+    </Metadata>
+</NEKTAR>
diff --git a/config_files/vvuq_example/vvuq_parameters.txt b/config_files/vvuq_example/vvuq_parameters.txt
new file mode 100644
index 0000000..8ca9311
--- /dev/null
+++ b/config_files/vvuq_example/vvuq_parameters.txt
@@ -0,0 +1,17 @@
+{
+ "parameters":
+ {"NUMBER_PARTICLES" : [40000],
+  "INIT_VELOCITY" : [1.0,0.9,1.1],
+  "CHARGE_DENSITY" : [105,101,109],
+  "NUMBER_DENSITY" : [105],
+  "TIME_STEPS" : [180],
+  "WRITE_FIELD_STEPS": [100],
+  "LINE_STEP": [20],
+  "LINE_NUMX": [100],
+  "LINE_NUMY": [1],
+ },
+ "output_columns": [
+  "Step#160/FIELD_EVALUATION_0",
+  "Step#160/x",
+ ]
+}
diff --git a/requirements.txt b/requirements.txt
index 167df30..eae1bf5 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,2 +1,4 @@
 h5py>=3.10.0
 PyVBMC>=1.0.1
+easyvvuq>=1.2
+chaospy>=4.3.2

From ea9848c740127d44157d13fb9d20e80d313850c8 Mon Sep 17 00:00:00 2001
From: Duncan Leggat <ccaedle@ucl.ac.uk>
Date: Tue, 13 Feb 2024 11:24:19 +0000
Subject: [PATCH 2/3] Altering vvuq run script to not include the file copying.
 This is now done in a temp directory within the function

---
 FabNESO/run_vvuq_instance.sh | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/FabNESO/run_vvuq_instance.sh b/FabNESO/run_vvuq_instance.sh
index 74e6414..5209d6e 100755
--- a/FabNESO/run_vvuq_instance.sh
+++ b/FabNESO/run_vvuq_instance.sh
@@ -1,9 +1,5 @@
 #!/usr/bin/env bash
 
-echo fabsim $1 single_run_vvuq:$PWD,solver=$4,processes=$5,nodes=$6,cpus_per_process=$7,wall_time=$8,neso_outfile=$9
+echo fabsim $1 single_run_vvuq:$PWD,mesh_file=$3,solver=$4,processes=$5,nodes=$6,cpus_per_process=$7,wall_time=$8,neso_outfile=$9
 
-pwd
-
-cp $3 .
-
-fabsim $1 single_run_vvuq:$PWD,solver=$4,processes=$5,nodes=$6,cpus_per_process=$7,wall_time=$8,neso_outfile=$9
+fabsim $1 single_run_vvuq:$PWD,mesh_file=$3,solver=$4,processes=$5,nodes=$6,cpus_per_process=$7,wall_time=$8,neso_outfile=$9

From 4daa70124928a631c1b842e100ee52a53d37fa27 Mon Sep 17 00:00:00 2001
From: Duncan Leggat <ccaedle@ucl.ac.uk>
Date: Tue, 13 Feb 2024 11:26:53 +0000
Subject: [PATCH 3/3] Adding a temporary config directory to the VVUQ run, and
 fixing typos

---
 FabNESO/tasks.py | 60 ++++++++++++++++++++++++++++--------------------
 1 file changed, 35 insertions(+), 25 deletions(-)

diff --git a/FabNESO/tasks.py b/FabNESO/tasks.py
index 913713e..b023c30 100644
--- a/FabNESO/tasks.py
+++ b/FabNESO/tasks.py
@@ -17,13 +17,6 @@
 import easyvvuq as uq
 import numpy as np
 import pyvbmc
-from easyvvuq.actions import (
-    Actions,
-    CreateRunDirectory,
-    Decode,
-    Encode,
-    ExecuteLocal,
-)
 
 try:
     from fabsim.base import fab
@@ -316,7 +309,7 @@ def neso_vbmc(  # noqa: PLR0913
     **vbmc_parameters: str,
 ) -> None:
     """
-    Run variational Bayesian Monte Carlo (VBMC) to calibrate NESO solver parametes.
+    Run variational Bayesian Monte Carlo (VBMC) to calibrate NESO solver parameters.
 
     The VBMC algorithm (Acerbi, 2018) is an approximate Bayesian inference method for
     efficient parameter calibration in expensive to simulate models. Here we use the
@@ -619,6 +612,7 @@ def _parse_vvuq_parameters(
 @fab.load_plugin_env_vars("FabNESO")
 def single_run_vvuq(
     config: str,
+    mesh_file: str = "mesh.xml",
     solver: str = "Electrostatic2D3V",
     processes: str | int = 4,
     nodes: str | int = 1,
@@ -639,6 +633,7 @@ def single_run_vvuq(
 
     Keyword Args:
         solver: Which NESO solver to use.
+        mesh_file_name: Name of mesh XML in configuration directory.
         processes: Number of processes to run.
         nodes: Number of nodes to run on. Only applicable when running on a multi-node
             system.
@@ -658,15 +653,26 @@ def single_run_vvuq(
             }
         )
 
-    # Run an instance of NESO
-    neso(
-        config,
-        solver=solver,
-        processes=processes,
-        nodes=nodes,
-        cpus_per_process=cpus_per_process,
-        wall_time=wall_time,
-    )
+    # Make a temporary directory to store the configs in - they can be deleted when the
+    # run is done
+    with TemporaryDirectory(dir=config) as temporary_config_dir:
+        config_path = Path(temporary_config_dir)
+
+        # Copy the mesh and conditions files here for FabSIM to read it properly
+        shutil.copyfile(mesh_file, config_path / Path(mesh_file).name)
+        shutil.copyfile("conditions.xml", config_path / "conditions.xml")
+
+        # Run an instance of NESO
+        neso(
+            temporary_config_dir,
+            solver=solver,
+            mesh_file_name=Path(mesh_file).name,
+            processes=processes,
+            nodes=nodes,
+            cpus_per_process=cpus_per_process,
+            wall_time=wall_time,
+        )
+
     # Retrieve the results
     fab.fetch_results()
 
@@ -683,7 +689,7 @@ def neso_vvuq_campaign(  # noqa: PLR0913
     vvuq_config: str,
     conditions_template: str = "conditions.template",
     vvuq_parameters: str = "vvuq_parameters.txt",
-    vvuq_script: str = "run_vvuq_instance.sh",
+    vvuq_script: str = "FabNESO/run_vvuq_instance.sh",
     neso_mesh_file: str = "mesh.xml",
     output_dir: str = "neso_pce/",
     neso_outfile: str = "Electrostatic2D3V_line_field_evaluations.h5part",
@@ -692,6 +698,8 @@ def neso_vvuq_campaign(  # noqa: PLR0913
     nodes: str | int = 1,
     cpus_per_process: str | int = 1,
     wall_time: str = "00:15:00",
+    *,
+    run_vvuq_sequential: bool = True,
 ) -> None:
     """
     Run a VVUQ campaign on a NESO solver.
@@ -719,6 +727,8 @@ def neso_vvuq_campaign(  # noqa: PLR0913
             applicable when running on a multi-node system.
         wall_time: Maximum time to allow job to run for. Only applicable when submitting
             to a job scheduler.
+        run_vvuq_sequential: Set to False to parallelise. Default is True because this
+            can cause issues if unchecked.
 
     """
     path_to_vvuq_configs = Path(fab.find_config_file_path(vvuq_config))
@@ -742,21 +752,21 @@ def neso_vvuq_campaign(  # noqa: PLR0913
     )
 
     # Get the path for this plugin,
-    vvuq_run_path = Path(fab.get_plugin_path("FabNESO")) / "FabNESO" / vvuq_script
+    vvuq_run_path = Path(fab.get_plugin_path("FabNESO")) / vvuq_script
 
     # The script that runs the individual NESO instances
-    execute_local = ExecuteLocal(
+    execute_local = uq.actions.ExecuteLocal(
         f"{vvuq_run_path} {fab.env.remote} {vvuq_config} "
         f"{path_to_vvuq_configs / neso_mesh_file} {solver} {processes} "
         f"{nodes} {cpus_per_process} {wall_time} {neso_outfile}"
     )
 
     # Put together the actions required for the VVUQ campaign
-    actions = Actions(
-        CreateRunDirectory("/tmp", flatten=True),  # noqa: S108
-        Encode(encoder),
+    actions = uq.actions.Actions(
+        uq.actions.CreateRunDirectory("/tmp", flatten=True),  # noqa: S108
+        uq.actions.Encode(encoder),
         execute_local,
-        Decode(decoder),
+        uq.actions.Decode(decoder),
     )
 
     # Make the VVUQ campaign
@@ -767,4 +777,4 @@ def neso_vvuq_campaign(  # noqa: PLR0913
     campaign.set_sampler(my_sampler)
 
     # Run VVUQ
-    campaign.execute(sequential=True).collate()
+    campaign.execute(sequential=run_vvuq_sequential).collate()